Impressions

Any cafe has its regulars, in Berlin the sparrows are the Stammgaeste everywhere, it seems, and I liked that.  They'll sweep up any crumbs and encourage you with a visit to your table as well (and your plate in some cases if you let them).
They're part of the city-scape which would be poorer without them.

Our choice of cafes: local cafe corner of Markgrafenstrasse and Rudi Dutschke Strasse, just south of the old Checkpoint Charlie border control and where the Wall once blighted Europe.  Used by locals - builders having a second breakfast, office workers collecting coffees 'to go', regulars dropping by - and tourists like us looking for a start to the day more authentic and cheaper than the tourist cafes around the Gendarmenmarkt a short walk away.
Around the Hackescher Markt, past the tourist trap bars right by the bridge, we found a corner cafe Italian-run with noodle salad and cappuccino, all for about 5 Euros each, and as importantly with a genuine feel to it, a place it's great to stumble on.

Prenzlauer Berg has a relaxed if gentrified feel, and Cafe Sowohl als Auch and Anna Blume, opposite each other near Kaethe Kollwitz Platz, both serve good food and drink in a lovely spot, sheltered but close to the street to watch people go by. A bit higher-priced but worth it.  Tip: don't ask at Anna Blume for the Apfel Strudel - they don't have it and disappear when asked!  Nice place otherwise though.

Hops and Barley is in alternative Friedrichshain and does a small range of tasty beers.  Next to M13 tram to Warschauer Strasse (this from the guide book).

Lehmke is also near Hackescher Markt and was pricier but the beer and ambience are traditional and reliable, the food a liitle less so.  Just missed the World Cup 7-1 win over Brazil ...